[Bioperl-l] PrimarySeq object question

[Heikki Lehvaslaiho]

Kevin,

The message you get comes from Bio::Seq::SeqWithQuality module. It could be 
argued that it is overzealous to throw an exception if it can not find a 
sequence. Also, the message comes after it has come to the conclusion that 
you have not set the alphabet that, according to your code snippet, you have. 
Report this as a bug to bugzilla.bioperl.org and make sure you attach an 
example scf file.

Meanwhile, you can always avoid exiting from you code by wrapping the code 
within the eval statement.

eval { 
  # your code   
}; # note the ';'
if ($@) {
  # do something else
}

Yours,
       -Heikki

On Thursday 08 December 2005 19:36, kevin.mcmahon at ttuhsc.edu wrote:
> Everyone,
>
> I'm new to this, so please bear with me.
>
> I'm having some trouble with a scf to fasta converting program I'm writing.
>
>   my $in  = Bio::SeqIO->new(-file => $infile , '-format' => 'scf',
> -alphabet => 'dna');
>
>     my $seq = $in->next_seq();
>     print "My sequence is:  " . $seq->seq() . "\n";
>
> Above is the code in discussion.  The $in object contains information from
> a file ($infile) in scf format.
>
> Here's my problem.  When we get to $in->next_seq(), if the file is empty,
> the program dies and returns:
>
> "MSG: If you want me to create a PrimarySeq object for your empty sequence
> <boggle> you must specify a -alphabet to satisfy the constructor
> requirements for a Bio::PrimarySeq object with no sequence.  Read the POD
> for it, luke."
>
> I guess what I need to know is: if this $in->next_seq() doesn't work, how
> can I test for this before I get this reply.
>
> Thanks in advance,
>
> Wyatt
>
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-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of the Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
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